243 Conserved Domain Database models. CDD 1 {"type": "domain"} 27 Density of coding genes, calculated by dividing the chromosome into 150 "bins" and counting the genes in each. (For very short chromosomes, e.g. MT, some genes contribute to multiple bins.) Coding genes (density) 1 \N 39 Dust is a program that identifies low-complexity sequences (regions of the genome with a biased distribution of nucleotides, such as a repeat). The Dust module is widely used with BLAST to prevent 'sticky' regions from determining false hits. Low complexity (Dust) 1 \N 2 Protein coding genes annotated in ENA Genes 1 {"label_key": "[biotype]", "caption": "Genes", "colour_key": "[biotype]", "default": {"cytoview": "gene_label", "MultiBottom": "collapsed_label", "alignsliceviewbottom": "as_collapsed_label", "MultiTop": "gene_label", "contigviewbottom": "transcript_label", "contigviewtop": "gene_label"}, "name": "Genes", "key": "ensembl"} 1 Assembly gap feature annotated in ENA Assembly gap (ENA) 1 \N 18 mRNA feature annotated in ENA mRNA (ENA) 1 {"caption": "Genomic features", "key": "ena_features", "label_key": "[text_label] [display_label]", "multi_name": "Genomic features", "name": "Genomic features"} 266 CATH/Gene3D families. Gene3D 1 {"type": "domain"} 3 Cross-references attached by GenomeLoader GenomeLoader cross-references 0 \N 272 \N GOA annotation 0 \N 46 GO term derived transitively from a UniProt record UniProt-derived GO term 0 \N 96 Gene encoding an enzyme annotated at the Plant Reactome. Plant Reactome 1 \N 246 HAMAP families. HAMAP 1 {"type": "domain"} 245 PANTHER families. PANTHER 1 {"type": "domain"} 268 InterPro2GO mapping, defined by InterPro. InterPro2GO mapping 0 \N 50 Density of long non-coding RNA genes, calculated by dividing the chromosome into 150 "bins" and counting the genes in each. (For very short chromosomes, e.g. MT, some genes contribute to multiple bins.) Long non-coding genes (density) 1 \N 257 Intrinsically disordered regions predicted by MobiDB lite. MobiDB lite 1 {"type": "feature"} 256 Coiled-coil regions predicted by Ncoils. Coiled-coils (Ncoils) 1 {"type": "feature"} 49 Percentage of repetitive elements for top level sequences (such as chromosomes, scaffolds, etc.) Repeats (percent) 1 \N 19 Percentage of G/C bases in the sequence. GC content 1 \N 250 Protein domains and motifs from the Pfam database. Pfam 1 {"type": "domain"} 267 Protein domains and motifs from the PROSITE profiles database. PROSITE profiles 1 {"type": "domain"} 248 Protein domains and motifs from the PIR (Protein Information Resource) Superfamily database. PIRSF 1 {"type": "domain"} 249 Protein fingerprints (groups of conserved motifs) from the PRINTS database. Prints 1 {"type": "domain"} 47 Density of pseudogenes, calculated by dividing the chromosome into 150 "bins" and counting the genes in each. (For very short chromosomes, e.g. MT, some genes contribute to multiple bins.) Pseudogenes (density) 1 \N 264 Repeats detected using Red (REPeatDetector) Repeats: Red 1 \N 41 Repeats detected using the MIPS Repeat Database (REdat) using RepeatMasker. Repeats: REdat 1 \N 42 Repeats identified by RepeatMasker, using the Repbase library of repeat profiles. Repeats: Repbase 1 \N 269 Protein domains and motifs from the PROSITE patterns database. PROSITE patterns 1 {"type": "domain"} 259 Low complexity peptide sequences identified by Seg. Low complexity (Seg) 1 {"type": "feature"} 252 Structure-Function Linkage Database families. SFLD 1 {"type": "domain"} 48 Density of short non-coding RNA genes, calculated by dividing the chromosome into 150 "bins" and counting the genes in each. (For very short chromosomes, e.g. MT, some genes contribute to multiple bins.) Short non-coding genes (density) 1 \N 258 Signal peptide cleavage sites predicted by SignalP. Cleavage site (Signalp) 1 {"type": "feature"} 254 Protein domains and motifs from the SMART database. SMART 1 {"type": "domain"} 253 Protein domains and motifs from the SUPERFAMILY database. Superfamily 1 {"type": "domain"} 255 Protein domains and motifs from the TIGRFAM database. TIGRFAM 1 {"type": "domain"} 262 Transmembrane helices predicted by TMHMM. Transmembrane helices 1 {"type": "feature"} 40 Tandem Repeats Finder locates adjacent copies of a pattern of nucleotides. Tandem repeats (TRF) 1 \N 43 UniParc mapping based on sequence checksums UniParc cross-reference 0 \N 44 UniProt cross-reference derived transitively from a UniParc identifier UniParc-derived cross-reference 0 \N 45 Cross-reference derived transitively from a UniProt record UniProt-derived cross-reference 0 \N 51 Cross references to UniProt Swiss-Prot (reviewed) proteins, determined by alignment against the proteome with blastp. UniProt reviewed proteins 0 \N